comments on new test version

[domenico-simone]

• Can the user decide the destination folder for the install.sh script?
• Can the user decide not to install some libraries/software installed by the install.sh script? eg if I already have a good system-wide gsnap installation, I'd not want to re-install it!
• Has the read maximum length issue solved by gsnap? If not, we could introduce an option in the install.sh for the gmap/gsnap compilation.

[domenico-simone]

Adding:

• we need to explain the sorting criteria for annotation.csv in the README.